DAS-NONE: Random small fixes. (#38)

No functional differences. Code cleanup and refactor
nasa · Dec 12, 2024 · 2f47607 · 2f47607
1 parent 2775c15
commit 2f47607
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diff --git a/.github/workflows/run_lib_tests.yml b/.github/workflows/run_lib_tests.yml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
       - name: Checkout harmony-browse-image-generator repository

diff --git a/.github/workflows/run_service_tests.yml b/.github/workflows/run_service_tests.yml
@@ -29,14 +29,8 @@ jobs:
       - name: Run test image
         run: ./bin/run-test
 
-      - name: Archive test results
+      - name: Archive test results and coverage
         uses: actions/upload-artifact@v4
         with:
-          name: Test results
-          path: test-reports/
-
-      - name: Archive coverage report
-        uses: actions/upload-artifact@v4
-        with:
-          name: Coverage report
-          path: coverage/*
+          name: reports
+          path: reports/**/*
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,10 +13,7 @@ repos:
     rev: v0.8.2
     hooks:
       - id: ruff
-        args: ["--fix", "--show-fixes", "--extend-select", "I"]
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.10.0
-    hooks:
-      - id: black-jupyter
-        args: ["--skip-string-normalization"]
-        language_version: python3.11
+        args: ["--fix", "--show-fixes"]
+        types_or: [python, jupyter]
+      - id: ruff-format
+        types_or: [python, jupyter]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,19 @@ HyBIG follows semantic versioning. All notable changes to this project will be
 documented in this file. The format is based on [Keep a
 Changelog](http://keepachangelog.com/en/1.0.0/).
 
+## [unreleased] - 2024-12-10
+
+### Changed
+
+* Changed pre-commit configuration to remove `black-jupyter` dependency [#38](https://github.com/nasa/harmony-browse-image-generator/pull/38)
+* Updates service image's python to 3.12 [#38](https://github.com/nasa/harmony-browse-image-generator/pull/38)
+* Simplifies test scripts to run with pytest and pytest plugins [#38](https://github.com/nasa/harmony-browse-image-generator/pull/38)
+
+### Removed
+
+* Removes `test_code_format.py` in favor of `ruff` pre-commit configuration [#38](https://github.com/nasa/harmony-browse-image-generator/pull/38)
+
+
 ## [v2.0.2] - 2024-10-15
 
 ### Fixed

diff --git a/bin/run-test b/bin/run-test
@@ -18,14 +18,14 @@ set -ex
 find . | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf
 
 # Make the directory into which XML format test reports will be saved
-mkdir -p test-reports
+mkdir -p reports/test-reports
 
 # Make the directory into which coverage reports will be saved
-mkdir -p coverage
+mkdir -p reports/coverage
 
 # Run the tests in a Docker container with mounted volumes for XML report
 # output and test coverage reporting
 docker run --platform linux/amd64 --rm \
-	-v $(pwd)/test-reports:/home/tests/reports \
-	-v $(pwd)/coverage:/home/tests/coverage \
+	-v $(pwd)/reports/test-reports:/home/reports/test-reports \
+	-v $(pwd)/reports/coverage:/home/reports/coverage \
 	ghcr.io/nasa/harmony-browse-image-generator-test "$@"
diff --git a/docker/service.Dockerfile b/docker/service.Dockerfile
@@ -15,7 +15,7 @@
 # and updates the entrypoint of the new service container
 #
 ###############################################################################
-FROM python:3.11
+FROM python:3.12
 
 WORKDIR "/home"
 

diff --git a/docs/HyBIG-Example-Usage.ipynb b/docs/HyBIG-Example-Usage.ipynb
@@ -230,7 +230,7 @@
    },
    "outputs": [],
    "source": [
-    "# if gdalinfo is installed you can see the palette associated with the PNG image.\n",
+    "# if gdalinfo is installed view the palette associated with the PNG image.\n",
     "!gdalinfo  hybig-output/example1/VCF5KYR_1991001_001_2018224205008.png"
    ]
   },
@@ -318,7 +318,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# If gdal is installed this will show you the corner points associated with the output files.\n",
+    "# If gdal is installed, show the corner points associated with the output files.\n",
     "!gdalinfo hybig-output/example2/ASTGTMV003_N00E022_dem.jpg | grep -E \"Left|Right\""
    ]
   },
@@ -690,7 +690,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.12.6"
   },
   "name": "HyBIG-Example-Usage.ipynb"
  },

diff --git a/harmony_service/adapter.py b/harmony_service/adapter.py
@@ -7,10 +7,8 @@
 
 """
 
-from os.path import basename
 from pathlib import Path
-from shutil import rmtree
-from tempfile import mkdtemp
+from tempfile import TemporaryDirectory
 
 from harmony_service_lib import BaseHarmonyAdapter
 from harmony_service_lib.message import Source as HarmonySource
@@ -73,7 +71,8 @@ def get_asset_from_item(self, item: Item) -> Asset:
         This is used to select which asset is used by HyBIG to generate
         the browse image following these steps:
 
-        1. If found, return the first asset with 'visual' in any of the item's values' roles.
+        1. If found, return the first asset with 'visual' in any of the item's
+           values' roles.
         2. If found, return the first asset that has 'data' in its item's values' roles.
         3. Raise a StopIteration error.
 
@@ -93,61 +92,59 @@ def get_asset_from_item(self, item: Item) -> Asset:
 
     def process_item(self, item: Item, source: HarmonySource) -> Item:
         """Processes a single input STAC item."""
-        try:
-            working_directory = mkdtemp()
-            results = item.clone()
-            results.assets = {}
-
-            asset = self.get_asset_from_item(item)
-
-            color_palette = get_color_palette_from_item(item)
-
-            # Download the input:
-            input_data_filename = download(
-                asset.href,
-                working_directory,
-                logger=self.logger,
-                cfg=self.config,
-                access_token=self.message.accessToken,
-            )
+        with TemporaryDirectory() as working_directory:
+            try:
+                results = item.clone()
+                results.assets = {}
+
+                asset = self.get_asset_from_item(item)
+
+                color_palette = get_color_palette_from_item(item)
+
+                # Download the input:
+                input_data_filename = download(
+                    asset.href,
+                    working_directory,
+                    logger=self.logger,
+                    cfg=self.config,
+                    access_token=self.message.accessToken,
+                )
 
-            # Create browse images.
-            image_file_list = create_browse_imagery(
-                self.message,
-                input_data_filename,
-                source,
-                color_palette,
-                logger=self.logger,
-            )
+                # Create browse images.
+                image_file_list = create_browse_imagery(
+                    self.message,
+                    input_data_filename,
+                    source,
+                    color_palette,
+                    logger=self.logger,
+                )
 
-            # image_file_list is a list of tuples (image, world, auxiliary)
-            # we need to stage them each individually, and then add their final
-            # locations to a list before creating the stac item.
-            item_assets = []
-
-            for (
-                browse_image_name,
-                world_file_name,
-                aux_xml_file_name,
-            ) in image_file_list:
-                # Stage the images:
-                browse_image_url = self.stage_output(browse_image_name, asset.href)
-                browse_aux_url = self.stage_output(aux_xml_file_name, asset.href)
-                world_file_url = self.stage_output(world_file_name, asset.href)
-                item_assets.append(('data', browse_image_url, 'data'))
-                item_assets.append(('metadata', world_file_url, 'metadata'))
-                item_assets.append(('auxiliary', browse_aux_url, 'metadata'))
-
-            manifest_url = self.stage_manifest(image_file_list, asset.href)
-            item_assets.insert(0, ('data', manifest_url, 'metadata'))
-
-            return self.create_output_stac_item(item, item_assets)
-
-        except Exception as exception:
-            self.logger.exception(exception)
-            raise HyBIGServiceError from exception
-        finally:
-            rmtree(working_directory)
+                # image_file_list is a list of tuples (image, world, auxiliary)
+                # we need to stage them each individually, and then add their final
+                # locations to a list before creating the stac item.
+                item_assets = []
+
+                for (
+                    browse_image_name,
+                    world_file_name,
+                    aux_xml_file_name,
+                ) in image_file_list:
+                    # Stage the images:
+                    browse_image_url = self.stage_output(browse_image_name, asset.href)
+                    browse_aux_url = self.stage_output(aux_xml_file_name, asset.href)
+                    world_file_url = self.stage_output(world_file_name, asset.href)
+                    item_assets.append(('data', browse_image_url, 'data'))
+                    item_assets.append(('metadata', world_file_url, 'metadata'))
+                    item_assets.append(('auxiliary', browse_aux_url, 'metadata'))
+
+                manifest_url = self.stage_manifest(image_file_list, asset.href)
+                item_assets.insert(0, ('data', manifest_url, 'metadata'))
+
+                return self.create_output_stac_item(item, item_assets)
+
+            except Exception as exception:
+                self.logger.exception(exception)
+                raise HyBIGServiceError(str(exception)) from exception
 
     def stage_output(self, transformed_file: Path, input_file: str) -> str:
         """Generate an output file name based on the input asset URL and the
@@ -174,7 +171,7 @@ def create_output_stac_item(
         """Create an output STAC item used to access the browse imagery and
             ESRI world file as staged in S3.
 
-        asset_items are an array of tuples where the tuples should be: (name,
+        item_assets is an array of tuples where the tuples should be: (name,
         url, role)
 
         """
@@ -191,7 +188,7 @@ def create_output_stac_item(
 
             output_stac_item.assets[asset_name] = Asset(
                 url,
-                title=basename(url),
+                title=Path(url).name,
                 media_type=get_file_mime_type(url),
                 roles=[role],
             )

diff --git a/harmony_service/utilities.py b/harmony_service/utilities.py
@@ -21,7 +21,7 @@ def get_tiled_file_extension(file_name: Path) -> str:
     generate the correct one to pass in.
 
     """
-    ext_pattern = r"(\.r\d+c\d+)?\.(png|jpg|pgw|jgw|txt)(.aux.xml)?"
+    ext_pattern = r'(\.r\d+c\d+)?\.(png|jpg|pgw|jgw|txt)(.aux.xml)?'
     match = re.search(ext_pattern, file_name.name)
     return match.group()
 
@@ -34,7 +34,7 @@ def get_asset_name(name: str, url: str) -> str:
     dictionary.
 
     """
-    tiled_pattern = r"\.(r\d+c\d+)\."
+    tiled_pattern = r'\.(r\d+c\d+)\.'
     tile_id = re.search(tiled_pattern, url)
     if tile_id is not None:
         name = f'{name}_{tile_id.groups()[0]}'

diff --git a/hybig/browse_utility.py b/hybig/browse_utility.py
@@ -21,14 +21,14 @@ def get_harmony_message_from_params(params: dict | None) -> HarmonyMessage:
 
     return HarmonyMessage(
         {
-            "format": {
-                "mime": mime,
-                "crs": crs,
-                "srs": crs,
-                "scaleExtent": scale_extent,
-                "scaleSize": scale_size,
-                "height": height,
-                "width": width,
+            'format': {
+                'mime': mime,
+                'crs': crs,
+                'srs': crs,
+                'scaleExtent': scale_extent,
+                'scaleSize': scale_size,
+                'height': height,
+                'width': width,
             },
         }
     )
diff --git a/hybig/crs.py b/hybig/crs.py
@@ -54,9 +54,9 @@ def choose_crs_from_srs(srs: SRS):
 
     """
     try:
-        if srs.epsg is not None and srs.epsg != "":
+        if srs.epsg is not None and srs.epsg != '':
             return CRS.from_string(srs.epsg)
-        if srs.wkt is not None and srs.wkt != "":
+        if srs.wkt is not None and srs.wkt != '':
             return CRS.from_string(srs.wkt)
         return CRS.from_string(srs.proj4)
     except Exception as exception:

diff --git a/hybig/exceptions.py b/hybig/exceptions.py
@@ -2,7 +2,7 @@
 
 
 class HyBIGError(Exception):
-    """Base error class for exceptions rasied by HyBIG library."""
+    """Base error class for exceptions raised by HyBIG library."""
 
     def __init__(self, message=None):
         """All HyBIG errors have a message field."""

diff --git a/hybig/sizes.py b/hybig/sizes.py
@@ -79,29 +79,29 @@ class Dimensions(TypedDict):
 
 # This is Table 4.1.8-1 WGS84 (EPSG: 4326 Resolutions)
 epsg_4326_resolutions = [
-    ResolutionInfo("2km", 0.017578125, 10240, 20480, 6, 2),
-    ResolutionInfo("1km", 0.0087890625, 20480, 40960, 7, 2),
-    ResolutionInfo("500m", 0.00439453125, 40960, 81920, 8, 2),
-    ResolutionInfo("250m", 0.002197265625, 81920, 163840, 9, 2),
-    ResolutionInfo("125m", 0.0010986328125, 163840, 327680, 10, 2),
-    ResolutionInfo("62.5m", 0.00054931640625, 327680, 655360, 11, 2),
-    ResolutionInfo("31.25m", 0.000274658203125, 655360, 1310720, 12, 2),
-    ResolutionInfo("15.625m", 0.0001373291015625, 1310720, 2521440, 13, 2),
+    ResolutionInfo('2km', 0.017578125, 10240, 20480, 6, 2),
+    ResolutionInfo('1km', 0.0087890625, 20480, 40960, 7, 2),
+    ResolutionInfo('500m', 0.00439453125, 40960, 81920, 8, 2),
+    ResolutionInfo('250m', 0.002197265625, 81920, 163840, 9, 2),
+    ResolutionInfo('125m', 0.0010986328125, 163840, 327680, 10, 2),
+    ResolutionInfo('62.5m', 0.00054931640625, 327680, 655360, 11, 2),
+    ResolutionInfo('31.25m', 0.000274658203125, 655360, 1310720, 12, 2),
+    ResolutionInfo('15.625m', 0.0001373291015625, 1310720, 2521440, 13, 2),
 ]
 
 # Conversion used above: resolution / pixel_size
 METERS_PER_DEGREE = 113777.77777777778
 
 # This is Table 4.1.8-2 NSIDC Sea Ice Polar Stereographic Extent (EPSG:3413) Resolutions
 epsg_3413_resolutions = [
-    ResolutionInfo("2km", 2048, 4096, 4096, 3, 2),
-    ResolutionInfo("1km", 1024, 8192, 8192, 4, 2),
-    ResolutionInfo("500m", 512, 16384, 16384, 5, 2),
-    ResolutionInfo("250m", 256, 32768, 32768, 6, 2),
-    ResolutionInfo("125m", 128, 65536, 65536, 7, 2),
-    ResolutionInfo("62.5m", 64, 131072, 131072, 8, 2),
-    ResolutionInfo("31.25m", 32, 252144, 252144, 9, 2),
-    ResolutionInfo("15.625m", 16, 524288, 524288, 10, 2),
+    ResolutionInfo('2km', 2048, 4096, 4096, 3, 2),
+    ResolutionInfo('1km', 1024, 8192, 8192, 4, 2),
+    ResolutionInfo('500m', 512, 16384, 16384, 5, 2),
+    ResolutionInfo('250m', 256, 32768, 32768, 6, 2),
+    ResolutionInfo('125m', 128, 65536, 65536, 7, 2),
+    ResolutionInfo('62.5m', 64, 131072, 131072, 8, 2),
+    ResolutionInfo('31.25m', 32, 252144, 252144, 9, 2),
+    ResolutionInfo('15.625m', 16, 524288, 524288, 10, 2),
 ]
 
 # The Antarctic resolutions match the northern resolutions precisely.

diff --git a/pyproject.toml b/pyproject.toml
@@ -50,3 +50,17 @@ exclude = [
 
 [tool.hatch.build.targets.wheel]
 packages=["hybig"]
+
+[tool.ruff]
+lint.select = [
+  "E",   # pycodestyle
+  "F",   # pyflakes
+  "UP",  # pyupgrade
+  "I",   # organize imports
+]
+
+[tool.ruff.format]
+quote-style = "single"
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"